User: Prashantha Hebbar

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Posts by Prashantha Hebbar

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Comment: C: Converting single GRanges object as per chromosome GRangeList
... Thank you. It works perfectly fine. Regards, Prashantha On Tuesday, December 3, 2013 8:18 PM, Steve Lianoglou wrote: Hi, On Tue, Dec 3, 2013 at 6:35 AM, Prashantha Hebbar wrote: [snip] > If I have my geneRange information as per chromosome in GRangeList form, my script becomes more effi ...
written 5.5 years ago by Prashantha Hebbar260
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Converting single GRanges object as per chromosome GRangeList
... Dear Friends, My following geneRange object has all chromosomal information in one GRange object. library(VariantAnnotation) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb = TxDb.Hsapiens.UCSC.hg19.knownGene txg = transcriptsBy(txdb,by="gene") > geneRange <- sort(unlist(range(txg[as.chara ...
snp go convert written 5.5 years ago by Prashantha Hebbar260 • updated 5.5 years ago by Steve Lianoglou12k
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Help on sapply() with GRanges
... Hello friends, I am trying to get genome cordinate information for list of genes using sapply function. I find an error saying " Error in c(values, x) : all arguments in '...' must be CompressedList objects " Following is the code I am using. library(VariantAnnotation) library(TxDb.Hsapiens.UCS ...
written 5.6 years ago by Prashantha Hebbar260 • updated 5.6 years ago by Michael Lawrence11k
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Way to extract population specific genotype from 1000 genome
... Hello friends, I have list of 120 genes and associated SNPs information of a cancer and want to find selection pressure in specific population using SNP information from 1000 genome. To do that I need genotype information for SNPs present in those genes from 1000 genome. Hence, any sort of suggesti ...
snp cancer written 5.9 years ago by Prashantha Hebbar260 • updated 5.9 years ago by Vincent J. Carey, Jr.6.3k
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Is there any way to merge all yeilds of FastqStreamer?
... Hello friends, I wanted to know a way to merge all yeilds of FastqStreamer as one ShortReadQ object. Can anybody suggestme a way to do this? readFq <- lapply(paste(inDataPath,fqFiles,sep=""),                         function(fqFiles){                                 fQ <-FastqStreamer(fqFile ...
written 7.4 years ago by Prashantha Hebbar260 • updated 7.4 years ago by Martin Morgan ♦♦ 23k
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About Multicore: mclapply
... Hello friends, I was tryig to parallize a function using mclapply. But I find lapply() executes in lesser time than mclapply(). I have given here my system time taken for both the functions. >library(ShortRead) >library(multicore)> fqFiles <- list.files("./test") > system.time(lapply( ...
written 7.4 years ago by Prashantha Hebbar260
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Answer: A: Help on ChIPpeakAnno
... Dear all, I have few issues with TSS information obtained through ChIPpeakAnno. To catalog TSS information pertaining to my probe sets I have used TSS.human.GRCh37 (ensemble) build. After obtaining information, data in the columns distanceToFeature and shorstestDistance do not exactly match with ei ...
written 8.3 years ago by Prashantha Hebbar260
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Help on ChIPpeakAnno
... Dear all, I have few issues with TSS information obtained through ChIPpeakAnno. To catalog TSS information pertaining to my probe sets I have used TSS.human.GRCh37 (ensemble) build. After obtaining information, data in the columns distanceToFeature and shorstestDistance do not exactly match with ei ...
probe chippeakanno written 8.3 years ago by Prashantha Hebbar260
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Is there any way to get upstream and downstream gene symbol?
... Dear Friends, I have to catalog upstream and downstream gene symbols of list of chromosomal co-ordinates. Can you please suggest me which package in bioconductor would help me to fetch up and downstream gene symbols provided chromosomal co- ordinates? Regards, Prashantha Hebbar Kiradi, Email:pra ...
written 8.5 years ago by Prashantha Hebbar260 • updated 8.5 years ago by Martin Morgan ♦♦ 23k
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Error while ChIPpeakAnno installation
... Dear Friends, I found an error during ChIPpeakAnno installation. Following is that error message. > biocLite("ChIPpeakAnno") Using R version 2.9.2, biocinstall version 2.4.13. Installing Bioconductor version 2.4 packages: [1] "ChIPpeakAnno" Please wait... Warning in install.packages(pkgs = pkgs ...
limma biomart iranges chippeakanno written 8.7 years ago by Prashantha Hebbar260 • updated 8.7 years ago by Julie Zhu4.0k

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